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Friday, 22 January 2016

In the growing world of free open-source software (FOSS) support often comes from online user forums. The quality of those forums can vary in terms of how many people reply to questions but, even in the best of them, a poorly phrased query will not be answered.

I spend a lot of time answering questions on the PsychoPy users forum where users of the PsychoPy stimulus presentation package can get and give help on how to create and improve their experiments. That forum is very active and a lot of people are willing to answer questions.

So why, you might ask, did your question not get an answer? Well, it might be that the timing was bad and everyone was busy, or that you had a great question but nobody knows the answer, but here are some tips to giving your question the best chance of being answered.

The key is that the people answering questions are doing so in their spare time. Most open source software is free and supported by volunteers with day jobs; that's why the software you downloaded was free. Those volunteers are generally willing to answer a question that will only take a few minutes to write. You need to make it easy for them. You need to write something that can be answered and preferably in a short email. Here are some examples of posts that cannot be answered and will typically lead to your question being ignored:

I want to use your software but I don't know how. Could somebody give me a working version of what I need? Presumably this will take more than 2 minutes so, unless the software only has 10 users, the answer is "No, it isn't possible for us to create it for you".

I created a script but it doesn't work. Any ideas? Could you give us a clue? If I ask you "Why is there no image on my TV?" you wouldn't be able to help me. There are too many possible options. What do you mean by "doesn't work"? What have you tried and what happened (for each option you tried)?

So, if some questions are not going to get an answer, how do you write a post that will? Partly you need to know how to troubleshoot the software and your script.

Know the basics and use Google first

If you can't use the basic functions of the software yet then you need to start with the documentation or go on a training course. For PsychoPy see the PsychoPy training resouces page. It's fine to announce that you're a "newbie" but implicitly announcing that you haven't looked at the documentation yet will get you ignored.

A huge number of questions have been answered before, and Google is pretty good at finding the previous answers. In particular, you could try using the error message that appeared in your Google search, but simple text of what you aimed to do might work too. Google really is amazing.

Expand on "it doesn't work"

The phrase "it doesn't work" almost never gives enough information. Check your email for that phrase and replace all instances with something more informative.

What happens when it doesn't work? Does the software crash? Is there an error message? (For PsychoPy) does the stimulus simply not show up? Some people will write "I've tried 4 different ways and none of them worked" but that still doesn't help. What happened for each one?

Explain what is different about your case compared to most others

If you're using software that is popular then in most cases it must be working. If it isn't working in your case then you should think a little about what might be different. Do you have any unusual computer hardware (e.g. a display that's unusually large)? Is the operating system set up in a different way (e.g. you use Urdu whereas most users are using American)?

Does the software provide demos and if so do they work? If none of them work then we could rule out your own coding as the problem. If some of them work then we can narrow down the problem. If they mostly do work then maybe the problem is with your own script.

Are there things that you are doing that are particularly unusual? Are you adding custom code? Are you trying to get unusually short durations for something? Quite often a post on the PsychoPy forum will say that "PsychoPy freezes when I present text" and after several iterations it turns out that the user had written their own custom code for presenting text that used a never-ending loop. Is it possible that your code was the problem, rather than the software?

Anything that you customized needs explaining and probably needs you to paste the precise details (e.g. code).

Don't write too much irrelevant detail

Although you need to provide enough detail for your query to be answered, if you write a really long post with a lot of irrelevant detail, or if you provide your entire 900-line script, nobody will have time to read the post at all.

So, the key is how to give enough detail that it can be answered, and not so much that it will be ignored. What counts as important will differ from one package to the next. For PsychoPy the following are nearly always important:

are you using code or Builder to create your study?

what version of PsychoPy do you have installed (and have you customised that in any way?)

what operating system?

The best way to give just enough, but not too much, detail is to give a minimal working example of the problem. That, ultimately is the aim, but that might warrant a separate blog post.

Just to reiterate, following this advice doesn't mean your question will absolutely get answered. I've seen perfectly good questions go unanswered on the PsychoPy list, often because I (and presumably others) just did not know the answer, or it was going to take a while to work out (sorry!) but the tips above will give you the best chance.

Sunday, 6 October 2013

I just read a dreadful article by John Bohannon about dubious scientific practice that, itself, contained a pretty basic logical/scientific error.

Bohannon explains that he conducted a "sting" operation where he sent a set of spoof papers, containing deliberate and obvious flaws, to a large number of Open Access journals and 157 of the 304 journals accepted the article (he goes on to use a few selective variants to make the percentages look bigger, but let's agree that over 50% failure to detect the spoof article is already quite a bad record).

All well and good so far. We already know that peer-review is flawed (a google search for problems with peer review raises 39 million hits) due partly to the fact that many journals are run as profit-making entities. This data highlights that nicely. Now, the problem lies in Bohannon's implicit claim that this is caused by open access. He makes this claim carefully with phrases like, "reveals little or no scrutiny at many open-access journals" and says that his data raise, "questions about peer-review practices in much of the open-access world". These phrases are designed carefully to put in your mind that the problem is with open access, but note that he doesn't explicitly state that. He can claim afterwards that he only specified open access because that's the only domain for which he has data. But let's be clear, he intends to imply that open access is the cause.

Probably many of you have already spotted the issue here. Most of the comments following the article point it out. Certainly Bohannon himself understood it, which is why the digs highlighted above are phrased so carefully. But let's just spell it out with a study of analogous logic. If you were to run a study showing that nearly all men have ears, you don't get to claim afterwards that ears seem to be a feature of being male. You don't even get to imply that result from your data. To say anything about whether ears are a male-specific feature you also have to measure their occurrence in non-males. You might be right - ears might turn out to be a male feature - and when you have data to show that their occurrence in women is less common then feel free to discuss that. But not before then.

This is a basic scientific error, and a man claiming to be identifying problems in our scientific culture should be embarrassed to be making such deliberately misleading statements.

Friday, 5 July 2013

Last week, for the first time, I published a paper for which I also uploaded all the electronic materials needed to replicate the study (for a moderately experienced vision scientist). You can now read about the fact that not only motion causes the silencing illusion of Suchow and Alvarez (I know you'll all be fascinated). But then you can also download the PsychoPy scripts to run the study, as well as analyse the original data and generate the plots. It may be surprising to the non-scientists out there that this is newsworthy but, in fact, almost nobody does this yet. I know! Unbelievable, right? Although scientists are mostly not shy about their findings, most are very shy about providing all the guts of their research, warts and all.

Some time ago I posted on the idea that we could do with an easy-to-use repository to which we could upload materials from experiments in psychology. There are numerous benefits for science in general, expanded on in the post above; we can create direct replications of other studies, we can spend more time thinking about scientific issues and less time rewriting basic stimulus code. I didn't express in that post that there's also a massive benefit for the publishing scientist, who is shy and territorial and doesn't want to lose the "competitive advantage". The perceived competitive advantage is that in this experimental topic (s)he's already written experiment code that nobody else has. But I believe it's massively outweighed by the benefit that when we publish our code we encourage more people to read our work and base their study on ours (to a geeky scientist that's the biggest complement you can pay). Let me put it another way: if your study was easy to program then somebody else can do it in no time (so no loss in giving them the code) and if the study was hard to program then they might never run the extension of it (so it's really important to give them the code so that they do).

Happily, unbeknownst to me when I wrote that post, the necessary repository was being created and you can now join up and use it at OpenScienceFramework.org. It's free, it's easy, it's permanent and it's easy on the eye. But it provides some great additional features. You can use it, before publishing your work, to share materials with your collaborators in a secure (private) repository and makes the materials available publicly later if you wish. The repository then has version control built-in so you can track changes to the materials, without needing to know about the underlying technologies. You can also use OpenScienceFramework to register in advance (again, privately) your intention to conduct a study and the expected outcomes in order to demonstrate which of your conclusions/analyses stem from genuinely a priori hypotheses.

Basically, this is a great resource that behavioural scientists should all be looking seriously. Many thanks to Brian Nosek, Jeff Spies and the rest of the OpenScienceFramework team. It is still in beta, so the creators are still taking feedback and adding features.

I'll be writing all my experiment code from now with the expectation that it will be published on OSF, and therefore writing it carefully with clearer-than-ever notes. For me this recent study is the first of (hopefully) many where you will be able to download the entire set of materials and data for the publication.

Tuesday, 29 May 2012

Increasingly, in all walks of life and all fields of work, performance now has to be quantified; we must all be given a number that identifies how good we are at whatever we do.

For academics we have the Research Excellence Framework (REF) exercise, which aims to measure the research performance of individual departments and whole universities, the National Student Survey (NSS) to measure the student experience and numerous newspaper league tables. In particular, the REF (formerly the Research Assessment Exercise, RAE) is a very influential performance indicator since it directly determines the distribution of one of the major funding sources for UK. It attracts a fair amount of comment as a result. See, for example, these informative posts calling the REF a time-wasting monster (Dorothy Bishop) and defending it (Andrew Derrington). Those articles have focused predominantly on whether the REF is good value for money (since it costs tens of millions of pounds to run).

I see a different problem with the REF, and also with all the other performance measures that are currently in use, which is that we simply have no idea how well the measures quantify what we want to know. All scientists know that in order to declare one treatment 'better' than another, we need not only a measure of its performance, but also an understanding of how good that measure is. None of us, beyond about first year undergraduate, would dream of presenting a mean without an error bar. We would also not give values beyond the number of decimal places that we can measure. We would certainly want to explain in our journal articles the caveats that should be taken into account to prevent people from over-interpreting our data.

Yet the REF, the NSS, and all of the newspaper league tables seem to be exempt from these things that all psychologists would consider good practice. So how do they 'measure up'? Are they reliable and precise? Do they even measure the thing they claim to [ed: 'valid', for the scientists in the readership]?

The authors of the posts above don't seem concerned about whether REF is an accurate measure. Dorothy Bishop's blog asserts that the REF yields no surprises (which would make it pointless but not inaccurate). Really? The top four or five might be obvious, but as you look down the list do you really find all those entries unsurprising? I don't want to name names, but I find it surprising how high some of those institutions appear to be, and similarly how low others are.

If I look at the tables of departments within my own field, rather than at the institutional ranks, I am very surprised indeed. I don't have any evidence to show that they are inaccurate or noisy other than my own experience (to quantify that we would need to conduct the exercise twice in quick succession with a new panel, which never occurs). But I certainly have my doubts about whether a REF rank of 10 is actually different to a REF rank of 15, say, or even 20. I mean 'significantly different' to use the same bar that we set for our scientific reporting. The question turns out to be incredibly important given the financial impact. In the newspaper league tables, which are created on much smaller budgets, my own department's ranking year-on-year changes enormously without any dramatic changes to the department or course.

Ok, so these measures might be somewhat noisy, but do they at least measure the thing we want? That isn't clear either. In the case of the REF we have no measure with which to compare other than our own personal judgements. And if the two disagree I suppose we have to decide that "the REF was based on more data than my opinion" so it wins. In fact, possibly the fact that Dorothy finds the tables unsurprising is that she has more experience (she certainly does). Without a gold standard, or any other metric at all for that matter, how do we decide whether REF is measuring the 'right' thing? We don't. We just hope. And when you hear that some universities are drafting in specialists to craft the documents for them, while other departments leave the job to whoever is their Director of Research, I suspect what we might be measuring is not how good an institution is at research, but how much they pay for their public relations people. How well they convince people or their worth and, possibly, how willing they are to 'accentuate' their assets.

Andrew Derrington (aka Russell Dean) points out that REF (and RAE) "seem to have earned a high degree of trust." I'm not sure who trusts it so much (possibly just the senior academic managers?) but even if it is trusted we know that doesn't mean it's good, right? It could well be the simple problem that people put far too much faith in a number when given one. Even highly competent scientists.

I think it's far from clear that the REF is measuring what we want, and even less that it's doing so accurately. But I should add that I don't have a better idea. I'm not saying we should throw the baby out with the bathwater. Maybe I'm just saying be careful about trying to interpret what a baby says.

Saturday, 19 May 2012

A lot of people ask me why I use Python instead of Matlab, or which is easier/better to learn. Maybe it's time I provided a comparison for psychology/neuroscience types to decide which language is better for them. Note that, although I write a prominent python package, this article is not aimed at trying to convert you. If Matlab works for you and makes you happy that's great! Personally, when I switched to Python I never looked back, and this explains a little about why.

Overall

Overall Python is a more flexible language and easier to read, and for me those two things are really important. Many people don't care whether their code is readable or clear for the future. They want it just to work now. For me, being able to understand the code again in a year's time is really important, and learning a new language wasn't too hard.

A lot of the differences between Matlab and Python come down to two things:

Matlab has a commercial, proprietary development model whereas Python is open-source. I won't go into that aspect much in this post. Some time I'll write a separate post about why I personally prefer the open-source model (they each have their benefits).

Matlab was designed to do maths but can be used more generally. Python was designed to be general but can be used for maths. That alters the way the languages work and the nature of the other users. That's also part of the reason that Python ships as part of Mac OS X and most Linux distributions. It's so generally useful it's made a part of the operating system.

Price and support

Price was certainly a part of my original decision to switch to Python. I was sick of setting up licenses, or getting blocked because the license server had too many users. Or needing to distribute processing to other machines, and discovering that they didn't all have the necessary (paid-for) toolboxes. But if it were just about the licensing I would have switched to Octave, a free alternative with almost identical syntax. The bigger issue I had was that I didn't actually like the language that much. Too many of the things that I felt should be core components of a language were bolt-on afterthoughts in Matlab.

Also at that point in time (2002-3) Mathworks was unsure if it would continue to support Apple Mac. I wanted to be able to choose what platform I used and not have that determined for me by Mathworks.

Generality

Ultimately there's little that Python can do that Matlab can't, and the converse is even more true. So why should it matter what they were originally designed for? Well, it does alter the decisions made by the programmers that built the systems. Matlab was designed to do maths and was extended to do much more; it was designed to be used by regular scientists not by programmers. Python was designed as a general language, that cold also do maths. On the whole that means that Matlab scripts/packages work very well for moderately complex tasks but they don't scale up very easily. Python might take a little more effort to get going, but saves you headaches in the long run.

Concrete examples? OK, just a couple.

How often in Matlab have you had some error message that made no sense that turned out to be caused by two functions on your path having the same name, or because you'd assigned a variable to the name of a function, and now that function doesn't work? Matlab assumes that everything on your path should be available at all times, because the developers didn't expect people to have hundreds of thousands of different functions on their path. Fair enough; if you only have 500 functions then giving each one a unique name is reasonable. Python is designed to have much larger numbers of libraries and functions installed, and the idea that each should need a unique name is quickly unworkable. So it becomes important that the entire path isn't constantly available in the 'namespace'. So in Python, like most other programming languages, you need to manually import the libraries that you want to use. That means a couple of extra lines at the start of your script but it also means you stand a better chance of avoiding name conflicts despite having a huge number of available functions in your libraries.

Python was designed from the ground-up to support object-oriented programming, with inheritance and dynamic updating of classes. For someone with experience in programming those things are incredibly useful allowing greater re-use of code and fewer bugs in large programs. For doing maths, object oriented programming seems less important and so the concept was rather late to appear in Matlab and the fact that it was bolted on as an afterthought shows.

Powerful syntax

I don't think there's any question that Python's syntax is superior to Matlab's. Some aspects might take you some getting used to (e.g. the fact that indices start at zero, or that correct indentation is a requirement). But in the end it has a huge number of features. Here a just a couple to give you the idea.

Fantastic string handling. Imagine being able to do things like this in Matlab:

>>> a='hello'
>>> b=' world'
>>> a+b #combine two strings? just add them!
'hello world'
>>> (a+b).title() #title is a method of all string objects
'Hello World'
>>> a==b #why would you want to write strcmp?!
False
>>> a>b
True
>>> str1="Strings can be surrounded by single or double quotes"
>>> str2='"Wow" and I can include the other type in the string?!'

Many things are easy in Python and considerably less readable in Matlab. Maybe they aren't important to you, but when you have very large scripts they can become a huge time-saver.

Available libraries

Although in science there are lots of Matlab users, which is great for sharing a script. What many people don't realise is that, overall, Python has many more users. So when you need help with, say, sound handling or importing some new file format, you are much more likely to find a ready-made library available for Python. That was another reason for me originally switching to Python; in early 2003 it already had a fully functional wrapper for OpenGL so I could use hardware-accelerated graphics directly from my scripts.

When I decided to build an editor and experiment builder GUI for PsychoPy I could do it all within Python, with relatively little effort, from existing Python libraries (e.g. wxPython). I can't imagine doing all that Matlab (although much of it would be technically possible it would be extremely painful).

When Microsoft changed the format of Excel files, soon enough there was a Python library (openpyxl) to read and write them, because an enthusiast went and created it. On Matlab, you still can't do that with a Mac, because Mathworks hasn't yet made that added it.

Ultimately

It is because of Python that I was able to write PsychoPy, and it's why other programmers have jumped on board the project. The clean easy syntax and the huge huge array of libraries allow normal people to write pretty professional applications.

Thursday, 8 March 2012

Do know those people that always start a conversation by telling you how busy they are? I don't mean occasionally. I mean the people that always seem to think they're impossibly busy.

"God I'm So Busy" people. Gisbies.

Think of some of the gisbies you know. What do you think of them? I've come to realise that I don't respect them. I tend to see them as less competent than my other non-gisbie colleagues. What I'm not sure about is why they annoy me so.

I think it's probably simply that I've noticed a correlation. The people in my life I've been most impressed by, those that excel in some way or another, never seem to complain about their time. But surely they are actually the most busy people I know; they're usually running departments or institutes or accomplishing ridiculous things in their spare time.

Gisbies, on the other hand, don't seem to be the people that are getting places and running the show. I actually suspect that the reason they're always telling me how busy they are is because they aren't so productive and they're worried people will think they aren't working. So they want to point out to everyone just how much they do.

And then they start implying that they do more than me. Are they really sure about that? I've got quite a few things going on that take up a lot of time. It's just that I'm not going around complaining about it. OK, sometimes I do, but when my plate is unusually full. Not always.

And then, to make matters worse, it seems like the gisbie actually delays my work by standing in my office telling me how busy they are!

In reality, I actually don't know what makes people into gisbies or why I dislike them. Probably a mixture of factors. But try not to tell me that you're too busy. I mean, not every time we meet.

Thursday, 16 February 2012

Have you ever read a psychology/neuroscience journal article and wondered if the information the authors had given you in the methods section was really sufficient for you to replicate the study?

Have you ever wanted to start a study with a new piece of software or something outside your normal method, and wished there was some existing experiment code that you could adapt for your needs?

A couple of people on the PsychoPy users list have suggested that it would be good to have a place to upload experimental code and materials to share.

It would serve a few purposes:

makes a study genuinely replicable, because you would be able to fetch the actual experiment as the authors used.

publicises an experiment that you've run because people could browse the repository looking for experiments they found interesting

provides a starting point for new users of a piece of software to build an experiment

The first goal can actually also be met by uploading your experiment to your own lab web pages, but that solution doesn't address the second and third points.

The repository would be agnostic to the subject of the study, and to the software used to run it. You would upload all the materials needed to run it (code, image files etc), tag which software package it was written for (PsychoPy, E-Prime, Presentation, Psychtoolbox etc...), provide a summary of what results should be expected and a reference to the paper showing the original (if published). Then you provide keywords about the topic that the experiment addresses so that people can browse or search for the experiment. Users might search by topic, keyword or software package to find experiments to learn from or replicate.

Potential issues

A few people have raised concerns about the idea:

Will it lead people to run studies that they didn't actually understand? For example, see this post on eagle-eyed-autism describing a study going badly wrong because the authors had borrowed code and hadn't really understood it. Is the answer to make sure it's very difficult to run studies, so that the scientist has to really know what you're doing in order to manage? That seems more than a little arrogant.

Will errors in studies propagate more? If a study has an error, when another lab writes it from scratch the error will likely not be made, but if they borrow and tweak the bug could propagate. I think the benefit that more eyes potentially examine the experiment and reduce the propagation of bugs.

Why should someone else simply take the experiment that I spent hours writing? To me this one just seems blatantly at odds with the aims and philosophy of science. But I guess some people will feel territorial like that.

People would never use such a site (unless forced) because they will be too embarrassed by the quality of their code, which was, after all designed to work without necessarily being elegant. I'm fairly sympathetic to this (although I've obviously shared many thousands of lines of my own code). But some people will be brave enough to expose their work fully, especially if it was generated by something like E-Prime or PsychoPy Builder, where the need actually to write code is reduced.

The idea is definitely growing on me, although I don't currently have the time to build the site, nor the funding to pay someone to build it.

I'm keen to hear more views. So feel free to comment below. Hopefully the idea will also be discussed as part of a satellite event on open-science at the Vision Sciences Society conference this May.